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Fluorine in PDB 4ybj: Type II Dasatinib Analog Crystallized with C-Src Kinase

Enzymatic activity of Type II Dasatinib Analog Crystallized with C-Src Kinase

All present enzymatic activity of Type II Dasatinib Analog Crystallized with C-Src Kinase:
2.7.10.2;

Protein crystallography data

The structure of Type II Dasatinib Analog Crystallized with C-Src Kinase, PDB code: 4ybj was solved by F.E.Kwarcinski, K.B.Brandvold, T.K.Johnson, S.Phadke, J.L.Meagher, M.A.Seeliger, J.A.Stuckey, M.B.Soellner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.56 / 2.61
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.117, 120.062, 63.319, 90.00, 90.26, 90.00
R / Rfree (%) 21.8 / 25

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Type II Dasatinib Analog Crystallized with C-Src Kinase (pdb code 4ybj). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Type II Dasatinib Analog Crystallized with C-Src Kinase, PDB code: 4ybj:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4ybj

Go back to Fluorine Binding Sites List in 4ybj
Fluorine binding site 1 out of 6 in the Type II Dasatinib Analog Crystallized with C-Src Kinase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Type II Dasatinib Analog Crystallized with C-Src Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:48.3
occ:1.00
 F3 A:4A9601 0.0 48.3 1.0
C11 A:4A9601 1.3 49.3 1.0
F1 A:4A9601 2.1 50.0 1.0
F2 A:4A9601 2.1 49.5 1.0
C10 A:4A9601 2.4 49.8 1.0
H8 A:4A9601 2.4 49.9 0.0
C12 A:4A9601 2.8 49.9 1.0
CD1 A:LEU317 3.6 42.5 1.0
C9 A:4A9601 3.7 49.9 1.0
CD1 A:LEU322 4.0 30.1 1.0
H7 A:4A9601 4.1 49.8 0.0
C13 A:4A9601 4.1 49.6 1.0
CE2 A:TYR382 4.2 41.4 1.0
CD2 A:HIS384 4.5 27.4 1.0
CD2 A:LEU322 4.7 31.8 1.0
CD2 A:TYR382 4.7 40.8 1.0
CG2 A:VAL377 4.8 26.8 1.0
CG A:LEU322 4.8 29.5 1.0
H9 A:4A9601 4.8 49.6 0.0
C8 A:4A9601 4.8 49.5 1.0
CG A:LEU317 4.9 43.4 1.0
CB A:LEU322 4.9 24.6 1.0
CZ A:TYR382 5.0 49.6 1.0
C14 A:4A9601 5.0 49.6 1.0

Fluorine binding site 2 out of 6 in 4ybj

Go back to Fluorine Binding Sites List in 4ybj
Fluorine binding site 2 out of 6 in the Type II Dasatinib Analog Crystallized with C-Src Kinase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Type II Dasatinib Analog Crystallized with C-Src Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:49.5
occ:1.00
 F2 A:4A9601 0.0 49.5 1.0
C11 A:4A9601 1.3 49.3 1.0
F1 A:4A9601 2.1 50.0 1.0
F3 A:4A9601 2.1 48.3 1.0
C10 A:4A9601 2.4 49.8 1.0
H7 A:4A9601 2.7 49.8 0.0
C9 A:4A9601 2.9 49.9 1.0
O A:VAL402 3.3 30.1 1.0
CB A:LEU322 3.5 24.6 1.0
C12 A:4A9601 3.6 49.9 1.0
CD1 A:LEU322 3.7 30.1 1.0
H8 A:4A9601 3.9 49.9 0.0
CG A:LEU322 4.0 29.5 1.0
CD2 A:LEU322 4.1 31.8 1.0
N A:VAL323 4.1 27.4 1.0
C A:VAL402 4.1 30.5 1.0
CA A:LEU322 4.2 24.3 1.0
C8 A:4A9601 4.3 49.5 1.0
O A:VAL323 4.4 33.0 1.0
C A:LEU322 4.5 30.0 1.0
CA A:ALA403 4.6 28.7 1.0
N A:ALA403 4.7 28.3 1.0
C13 A:4A9601 4.7 49.6 1.0
CG1 A:VAL402 4.8 28.3 1.0
CB A:VAL402 4.8 28.7 1.0
CD1 A:LEU317 5.0 42.5 1.0

Fluorine binding site 3 out of 6 in 4ybj

Go back to Fluorine Binding Sites List in 4ybj
Fluorine binding site 3 out of 6 in the Type II Dasatinib Analog Crystallized with C-Src Kinase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Type II Dasatinib Analog Crystallized with C-Src Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:50.0
occ:1.00
 F1 A:4A9601 0.0 50.0 1.0
C11 A:4A9601 1.3 49.3 1.0
F3 A:4A9601 2.1 48.3 1.0
F2 A:4A9601 2.1 49.5 1.0
C10 A:4A9601 2.4 49.8 1.0
C9 A:4A9601 3.2 49.9 1.0
H7 A:4A9601 3.3 49.8 0.0
C12 A:4A9601 3.3 49.9 1.0
CG1 A:VAL402 3.3 28.3 1.0
H8 A:4A9601 3.4 49.9 0.0
O A:VAL402 3.5 30.1 1.0
CD2 A:HIS384 3.5 27.4 1.0
NE2 A:HIS384 3.6 26.6 1.0
C A:VAL402 3.6 30.5 1.0
N A:ALA403 3.8 28.3 1.0
CA A:ALA403 3.9 28.7 1.0
CB A:VAL402 3.9 28.7 1.0
O A:ALA403 4.0 33.1 1.0
C A:ALA403 4.0 33.7 1.0
CA A:VAL402 4.4 25.0 1.0
C8 A:4A9601 4.4 49.5 1.0
C13 A:4A9601 4.5 49.6 1.0
CD2 A:LEU322 4.5 31.8 1.0
N A:ASP404 4.8 31.7 1.0
CG A:HIS384 4.8 26.3 1.0
CD1 A:LEU322 4.9 30.1 1.0
CE1 A:HIS384 4.9 26.2 1.0
C14 A:4A9601 4.9 49.6 1.0

Fluorine binding site 4 out of 6 in 4ybj

Go back to Fluorine Binding Sites List in 4ybj
Fluorine binding site 4 out of 6 in the Type II Dasatinib Analog Crystallized with C-Src Kinase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Type II Dasatinib Analog Crystallized with C-Src Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:49.2
occ:1.00
 F3 B:4A9601 0.0 49.2 1.0
C11 B:4A9601 1.3 48.4 1.0
F2 B:4A9601 2.1 46.9 1.0
F1 B:4A9601 2.1 49.0 1.0
C10 B:4A9601 2.4 48.8 1.0
C9 B:4A9601 3.1 48.9 1.0
H7 B:4A9601 3.2 49.0 0.0
NE2 B:HIS384 3.3 30.7 1.0
C12 B:4A9601 3.3 49.0 1.0
CD2 B:HIS384 3.4 31.2 1.0
CG1 B:VAL402 3.4 26.8 1.0
O B:ALA403 3.4 30.2 1.0
H8 B:4A9601 3.5 49.0 0.0
O B:VAL402 3.5 29.5 1.0
C B:ALA403 3.6 31.2 1.0
C B:VAL402 3.7 29.4 1.0
N B:ALA403 3.8 26.4 1.0
CA B:ALA403 3.8 26.7 1.0
CB B:VAL402 4.1 27.1 1.0
N B:ASP404 4.3 29.5 1.0
C8 B:4A9601 4.4 48.8 1.0
CB B:ASP404 4.5 32.3 1.0
CA B:VAL402 4.5 23.6 1.0
C13 B:4A9601 4.5 49.3 1.0
CE1 B:HIS384 4.5 30.2 1.0
CG B:LEU322 4.7 35.5 1.0
CG B:HIS384 4.7 29.9 1.0
CD2 B:LEU322 4.9 38.2 1.0
C14 B:4A9601 5.0 49.3 1.0
CA B:ASP404 5.0 30.1 1.0

Fluorine binding site 5 out of 6 in 4ybj

Go back to Fluorine Binding Sites List in 4ybj
Fluorine binding site 5 out of 6 in the Type II Dasatinib Analog Crystallized with C-Src Kinase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Type II Dasatinib Analog Crystallized with C-Src Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:46.9
occ:1.00
 F2 B:4A9601 0.0 46.9 1.0
C11 B:4A9601 1.3 48.4 1.0
F3 B:4A9601 2.1 49.2 1.0
F1 B:4A9601 2.1 49.0 1.0
C10 B:4A9601 2.4 48.8 1.0
H8 B:4A9601 2.5 49.0 0.0
C12 B:4A9601 2.8 49.0 1.0
C9 B:4A9601 3.7 48.9 1.0
CD1 B:LEU317 3.7 47.8 1.0
CD2 B:LEU322 3.8 38.2 1.0
H7 B:4A9601 4.1 49.0 0.0
CE2 B:TYR382 4.1 40.1 1.0
C13 B:4A9601 4.2 49.3 1.0
CG B:LEU322 4.2 35.5 1.0
CD2 B:HIS384 4.4 31.2 1.0
CD2 B:TYR382 4.7 39.5 1.0
NE2 B:HIS384 4.8 30.7 1.0
C8 B:4A9601 4.8 48.8 1.0
H9 B:4A9601 4.8 49.3 0.0
CZ B:TYR382 4.9 49.2 1.0
OH B:TYR382 4.9 50.3 1.0
CG2 B:VAL377 4.9 30.1 1.0
O B:VAL402 4.9 29.5 1.0
CG1 B:VAL402 4.9 26.8 1.0

Fluorine binding site 6 out of 6 in 4ybj

Go back to Fluorine Binding Sites List in 4ybj
Fluorine binding site 6 out of 6 in the Type II Dasatinib Analog Crystallized with C-Src Kinase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Type II Dasatinib Analog Crystallized with C-Src Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:49.0
occ:1.00
 F1 B:4A9601 0.0 49.0 1.0
C11 B:4A9601 1.3 48.4 1.0
F2 B:4A9601 2.1 46.9 1.0
F3 B:4A9601 2.1 49.2 1.0
C10 B:4A9601 2.4 48.8 1.0
H7 B:4A9601 2.7 49.0 0.0
C9 B:4A9601 2.9 48.9 1.0
O B:VAL402 3.1 29.5 1.0
CG B:LEU322 3.3 35.5 1.0
CD2 B:LEU322 3.4 38.2 1.0
C12 B:4A9601 3.6 49.0 1.0
H8 B:4A9601 3.9 49.0 0.0
C B:VAL402 3.9 29.4 1.0
CB B:LEU322 4.0 31.4 1.0
N B:VAL323 4.3 35.6 1.0
C8 B:4A9601 4.3 48.8 1.0
CA B:ALA403 4.4 26.7 1.0
CA B:LEU322 4.4 31.1 1.0
CD1 B:LEU322 4.4 35.0 1.0
N B:ALA403 4.5 26.4 1.0
CG1 B:VAL402 4.6 26.8 1.0
O B:VAL323 4.6 42.4 1.0
CB B:VAL402 4.7 27.1 1.0
C B:LEU322 4.7 37.1 1.0
C13 B:4A9601 4.7 49.3 1.0
C B:ALA403 4.8 31.2 1.0
CA B:VAL402 4.9 23.6 1.0

Reference:

F.E.Kwarcinski, K.R.Brandvold, S.Phadke, O.M.Beleh, T.K.Johnson, J.L.Meagher, M.A.Seeliger, J.A.Stuckey, M.B.Soellner. Conformation-Selective Analogues of Dasatinib Reveal Insight Into Kinase Inhibitor Binding and Selectivity. Acs Chem.Biol. V. 11 1296 2016.
ISSN: ESSN 1554-8937
PubMed: 26895387
DOI: 10.1021/ACSCHEMBIO.5B01018
Page generated: Sun Dec 13 12:15:50 2020

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